SARS1
seryl-tRNA synthetase 1, the group of Aminoacyl tRNA synthetases, Class II
Basic information
Region (hg38): 1:109213918-109238182
Previous symbols: [ "SARS" ]
Links
Phenotypes
GenCC
Source:
- autosomal recessive non-syndromic intellectual disability (Supportive), mode of inheritance: AR
- neurodevelopmental disorder with microcephaly, ataxia, and seizures (Moderate), mode of inheritance: AR
- neurodevelopmental disorder with microcephaly, ataxia, and seizures (Limited), mode of inheritance: AR
- neurodevelopmental disorder (Limited), mode of inheritance: AD
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Neurodevelopmental disorder with microcephaly, ataxia, and seizures | AR | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Musculoskeletal; Neurologic | 28236339 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (42 variants)
- not_provided (11 variants)
- Neurodevelopmental_disorder_with_microcephaly,_ataxia,_and_seizures (10 variants)
- SARS1-related_disorder (5 variants)
- Hyperuricemia,_pulmonary_hypertension,_renal_failure,_alkalosis_syndrome (2 variants)
- See_cases (1 variants)
- Cerebral_arteriovenous_malformation (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SARS1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000006513.4. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 9 | |||||
| missense | 47 | 50 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | |||||
| Total | 1 | 1 | 49 | 8 | 2 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SARS1 | protein_coding | protein_coding | ENST00000234677 | 11 | 24252 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.999 | 0.000749 | 125744 | 0 | 3 | 125747 | 0.0000119 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.66 | 170 | 299 | 0.568 | 0.0000170 | 3378 |
| Missense in Polyphen | 36 | 114.75 | 0.31372 | 1309 | ||
| Synonymous | 1.48 | 94 | 114 | 0.823 | 0.00000639 | 973 |
| Loss of Function | 4.70 | 2 | 29.6 | 0.0675 | 0.00000175 | 321 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000176 | 0.0000176 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Catalyzes the attachment of serine to tRNA(Ser) in a two-step reaction: serine is first activated by ATP to form Ser- AMP and then transferred to the acceptor end of tRNA(Ser) (PubMed:22353712, PubMed:24095058, PubMed:9431993, PubMed:26433229, PubMed:28236339). Is probably also able to aminoacylate tRNA(Sec) with serine, to form the misacylated tRNA L-seryl-tRNA(Sec), which will be further converted into selenocysteinyl-tRNA(Sec) (PubMed:9431993, PubMed:26433229, PubMed:28236339). In the nucleus, binds to the VEGFA core promoter and prevents MYC binding and transcriptional activation by MYC (PubMed:24940000). Recruits SIRT2 to the VEGFA promoter, promoting deacetylation of histone H4 at 'Lys-16' (H4K16). Thereby, inhibits the production of VEGFA and sprouting angiogenesis mediated by VEGFA (PubMed:19423848, PubMed:19423847, PubMed:24940000). {ECO:0000269|PubMed:19423847, ECO:0000269|PubMed:19423848, ECO:0000269|PubMed:22353712, ECO:0000269|PubMed:24095058, ECO:0000269|PubMed:24940000, ECO:0000269|PubMed:26433229, ECO:0000269|PubMed:28236339, ECO:0000269|PubMed:9431993}.;
- Disease
- DISEASE: Neurodevelopmental disorder with microcephaly, ataxia, and seizures (NEDMAS) [MIM:617709]: An autosomal recessive disorder characterized by delayed psychomotor development, intellectual disability, seizures apparent in infancy, impaired speech, and aggressive behavior. Additional features include microcephaly, ataxia, and muscle weakness. {ECO:0000269|PubMed:28236339}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Aminoacyl-tRNA biosynthesis - Homo sapiens (human);3-Phosphoglycerate dehydrogenase deficiency;Non Ketotic Hyperglycinemia;Glycine and Serine Metabolism;Dimethylglycine Dehydrogenase Deficiency;Hyperglycinemia, non-ketotic;Dimethylglycine Dehydrogenase Deficiency;Sarcosinemia;Dihydropyrimidine Dehydrogenase Deficiency (DHPD);tRNA Aminoacylation;Translation;Selenocysteine synthesis;Metabolism of proteins;Metabolism of amino acids and derivatives;Glycine Serine metabolism;selenocysteine biosynthesis;Metabolism;tRNA charging;Selenoamino acid metabolism;Cytosolic tRNA aminoacylation
(Consensus)
Recessive Scores
- pRec
- 0.261
Intolerance Scores
- loftool
- 0.145
- rvis_EVS
- -0.32
- rvis_percentile_EVS
- 31.69
Haploinsufficiency Scores
- pHI
- 0.190
- hipred
- Y
- hipred_score
- 0.749
- ghis
- 0.547
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.999
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Sars
- Phenotype
Zebrafish Information Network
- Gene name
- sars
- Affected structure
- trunk vasculature
- Phenotype tag
- abnormal
- Phenotype quality
- branchiness
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;translation;tRNA aminoacylation for protein translation;seryl-tRNA aminoacylation;tRNA processing;selenocysteine metabolic process;negative regulation of angiogenesis;selenocysteinyl-tRNA(Sec) biosynthetic process;negative regulation of vascular endothelial growth factor production
- Cellular component
- nucleus;cytoplasm;cytosol;extracellular exosome
- Molecular function
- RNA polymerase II proximal promoter sequence-specific DNA binding;RNA binding;serine-tRNA ligase activity;protein binding;ATP binding;protein homodimerization activity;selenocysteine-tRNA ligase activity